SLTM

protein-coding

SAFB like transcription modulator, the group of RNA binding motif containing

Gene summary

Enables RNA binding activity. Predicted to be involved in DNA-templated transcription and apoptotic process. Located in nuclear body. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_024755.4

Inheritance

—

ClinVar variants

P:1U:136

Top phenotype

Jeune thoracic dystrophy

gnomAD constraint

pLI —, LoF o/e 0.17

Max pathogenic AF

—

Genomic locus

chr15:58,879,050-58,933,679

External References & Databases

Ensembl (ENSG00000137776)

Transcript & Mutation Effects

hg38 • Region Span ~54.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SLTM variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 117

not providedTotal: 4

Jeune thoracic dystrophyTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_024755.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			3 clinvar			3
missense		1 clinvar	124 clinvar			125
nonsense			4 clinvar			4
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			5 clinvar			5
Total	0	1	136	0	0	137

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 87 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_024755.4	RefSeq	NP_079031.2	21	MANE Select
ENST00000380516.7	Ensembl	ENSP00000369887.2	21	MANE Select
NM_001013843.3	RefSeq	NP_001013865.1	21	Standard
ENST00000249736.11	Ensembl	ENSP00000249736.7	11	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of transcription by RNA polymerase II
apoptotic process
regulation of mRNA processing

Molecular Function

RNA binding
sequence-specific DNA binding

Cellular Component

nucleus
nucleoplasm
nuclear body

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000380516
Coding exons: 21
Length: 54609
Individuals with no LoFs: 125723
Homozygous LoFs: 0
Heterozygous LoFs: 25
Defined: 125748
p: 0.0000994

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.53	416	588	0.707	0.0000340	6798
Missense (PolyPhen)		82	116.14	0.70602		1146
Synonymous	0.137	197	199	0.988	0.0000110	1921
Loss of Function	6.30	11	66.5	0.165	0.00000471	693

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.00020	0.00020	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00027	0.00027	rare
Finnish	0.000047	0.000046	rare
European (Non-Finnish)	0.000053	0.000053	rare
South Asian	0.000034	0.000033	rare
Other	0.00065	0.00065	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: When overexpressed, acts as a general inhibitor of transcription that eventually leads to apoptosis. {ECO:0000250}.;

Recessive Scores

pRec: 0.133

Intolerance Scores

LoFtool: 0.267
RVIS EVS: -1.04
RVIS percentile EVS: 7.77

Essentials

Essential (CRISPR): E
Essential (CRISPR2): N
Essential (gene trap): K
Indispensability pred.: E
Indispensability score: 0.952

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium